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@sysbio-curie Computational Systems Biology of Cancer at Institut Curie

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    94 repositories

    • PhysiBoSSv1

      Public
      Multiscale simulation of multi-cellular system
      C++
      •
      Other
      •11•11•0•0•Updated Oct 2, 2024Oct 2, 2024

    • WebMaBoSS

      Public
      A web interface for MaBoSS modeling
      JavaScript
      •
      GNU Lesser General Public License v3.0
      •3•1•0•0•Updated Oct 2, 2024Oct 2, 2024

    • NaviCell

      Public
      A web tool for exploring large maps of molecular interactions
      Jupyter Notebook
      •
      GNU Lesser General Public License v3.0
      •1•10•0•16•Updated Oct 2, 2024Oct 2, 2024

    • MaBoSS

      Public
      MaBoSS is a C++ software for simulating continuous/discrete time Markov processes, applied on a Boolean network.
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •5•1•0•0•Updated Oct 2, 2024Oct 2, 2024

    • multipit

      Public
      Fusion strategies to build multimodal predictors for the prediction of immunotherapy response in non-small cell lung cancer
      Jupyter Notebook
      •
      MIT License
      •2•2•0•0•Updated Oct 2, 2024Oct 2, 2024

    • tipit_benchmark_RNA

      Public
      Benchmark of transcriptomic signatures for the prediction of immunotherapy response
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • Neko

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•8•0•0•Updated Sep 27, 2024Sep 27, 2024

    • PhysiBoSS

      Public
      PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks
      C++
      •92•1•0•0•Updated Sep 16, 2024Sep 16, 2024

    • NeKo_Supp_Mat

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Sep 16, 2024Sep 16, 2024

    • Invasion_model_NeKo

      Public
      This repo hosts all the notebooks and data needed to build a model of cell invasion automatically using NeKo.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 16, 2024Jul 16, 2024

    • stabilized-ica

      Public
      This repository proposes a python implementation of a stabilized ICA algorithm
      Python
      •
      MIT License
      •4•1•0•0•Updated Jul 3, 2024Jul 3, 2024

    • .github

      Public
      0•0•0•0•Updated Jul 3, 2024Jul 3, 2024

    • CFnetwork

      Public
      Codes to reproduce the analyses and the construction of the CF signalling network.
      R
      •1•0•0•0•Updated Jun 21, 2024Jun 21, 2024

    • CFnetwork_cytoscape

      Public
      Repository for the cytoscape session of the CF network paper
      R
      •0•0•0•0•Updated Jun 11, 2024Jun 11, 2024

    • hpcmaboss-artifact

      Public
      HPC MaBoSS artifact
      C++
      •
      MIT License
      •1•0•0•0•Updated May 7, 2024May 7, 2024

    • neko_dep

      Public
      Dependencies for Neko in case pypath download manager does not work properly.
      HTML
      •0•0•0•0•Updated May 7, 2024May 7, 2024

    • MaBoSS.GPU

      Public
      The GPU implementation of MaBoSS tool.
      C++
      •
      MIT License
      •2•0•0•0•Updated May 6, 2024May 6, 2024

    • KinaseSubstrateRelationship

      Public
      Other
      •0•0•0•0•Updated Mar 28, 2024Mar 28, 2024

    • PhysiBoSS_Old

      Public
      PhysiCell: Scientist end users should use latest release! Bugfixes should be submitted to the development branch.
      Jupyter Notebook
      •92•3•0•0•Updated Feb 6, 2024Feb 6, 2024

    • rROMA

      Public
      An r interface to perform ROMA (updated version 2022)
      HTML
      •
      GNU General Public License v3.0
      •0•2•2•0•Updated Dec 5, 2023Dec 5, 2023

    • rRoma_comp

      Public
      Repository for the comparison of sample-wise methods for the rRoma article
      R
      •0•0•0•0•Updated Oct 27, 2023Oct 27, 2023

    • PhysiMeSS

      Public
      PhysiCell MicroEnvironment Structure Simulation
      C++
      •92•0•0•0•Updated Oct 26, 2023Oct 26, 2023

    • transmorph

      Public
      Computational framework for dataset integration
      pipdata-integrationsingle-celloptimal-transportsingle-cell-rna-seqsingle-cell-analysispython
      Jupyter Notebook
      •
      MIT License
      •2•11•0•0•Updated Jul 21, 2023Jul 21, 2023

    • ICA-in-Cancer-research-review-materials

      Public
      jupyter-notebookicadeconvolution-methods
      Jupyter Notebook
      •0•2•0•2•Updated Jul 6, 2023Jul 6, 2023

    • Pypath_pipeline

      Public
      Automatic network construction using omnipath and pypath
      Jupyter Notebook
      •2•0•0•0•Updated Jun 29, 2023Jun 29, 2023

    • Curie-PerMedCoE-Summer-School-2023

      Public
      Jupyter Notebook
      •2•0•0•0•Updated Jun 27, 2023Jun 27, 2023

    • Invasion_model_PhysiBoSS

      Public
      Graphical interface for the Invasion model developed with PhysiBoSS. In the "Supp_Mat" section are stored the supplementary materials for the analysis and the description of the model.
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•0•Updated May 25, 2023May 25, 2023

    • topic_modeling_lncRNAs

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •2•2•0•0•Updated Apr 26, 2023Apr 26, 2023

    • paraExaStoLog

      Public
      Paralel implementation of "Exact calculator of Stochastic Logistic models"
      Cuda
      •1•0•0•0•Updated Apr 11, 2023Apr 11, 2023

    • MaBoSS-Review

      Public
      Notebook associated to the review about MaBoSS
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Mar 30, 2023Mar 30, 2023